People

Sophie Abby received a bi-disciplinary education in biology and computer sciences. She is an evolutionary biologist, particularly interested in the mechanisms of diversification of archaea and bacteria. She studies these at different scales: from enzymes and metabolic pathways, to macromolecular complexes and genome dynamics in response to environmental adaptations. She also develops methods in the field of comparative genomics and phylogenomics, in particular for genome annotation.

Ivan Junier is the resident biophycist expert. He works on rationalising the tinkering that has shaped the content, organisation and structuring of bacterial genomes. To this end, he develops quantitative, biophysical models of DNA in interaction with various fundamental proteins and molecular machineries that are crucial for gene expression, chromosome replication and chromosome segregation. To navigate in the (sometimes dark) space of bacterial genomes, he uses comparative genomics and statistical methods to distinguish between universal and idiosyncratic features.

Nelle Varoquaux is a machine.

Elham Ghobadpour is a postdoc working on Polymer physics modeling of bacterial chromosomes under the supervision of Ivan Junier.

Margaux Jullien is a postdoctoral researcher using bioinformatics to study coevolution in proteins. She previously worked on plant population and quantitative genetics.

Gabin Laurent is a postdoctoral researcher working on the physical modeling of DNA transcription and replication in bacteria.

Victor Bañon Garcia is a PHD student working on “Systematic study of inverted repeated sequences in prokaryotic genomes” under the supervision of Ivan Junier and Nelle Varoquaux.

Marion Chauveau is a PHD student working on Generative models for genome organisation under the supervision of Ivan Junier and Olivier Rivoire.

Sophie-Carole Chobert is a PhD candidate trained in bioinformatics. She is interested in the evolution of microorganisms and their adaptation to their environment. Her thesis focuses on a family of molecules with a key role in respiratory chains of most living organisms: the isoprenoid quinones. She aims at deciphering the origins and diversification of their biosynthetic pathways. She is supervised by Sophie Abby and Fabien Pierrel.

Lucas Etourneau is a PhD student funded by MIAI institute working in biostatistics and machine learning applied to mass-spectrometry based proteomic data. His thesis focuses on missing values inference in MNAR context, based on multi-omic integration. He also works on False Discovery Rate control and the general problem of variable selection in high dimensional setting. Thomas Burger from EDyP Lab and Nelle Varoquaux from CompBio@Tree supervise his thesis since 2020.

Flora Gaudillière is a PhD student working on the role of insertion sequences in the evolution and adaptation of prokaryotic genomes. She combines bioinformatic approaches with wet lab experiments. She is supervised by Ivan Junier and Thomas Hindré.

Sandy Frank Kwamou Ngaha is a PHD student working on the Detection of new secretion systems in collaboration with experts in these systems under the supervisions of Nelle VAROQUAUX and Sophie ABBY

Morgane Roger-Margueritat is a PhD student working on the impact of quinone exchanges on the gut microbiota. She combines experimental and bioinformatic approaches. She is supervised by Fabien Pierrel and Sophie Abby.

Zakaria Tougui is a PhD student working on the quantitative characterisation of the human gut microbiome, with a focus on the small intestine, combining publicly available data with data obtained from collaborators at TIMC using a newly developped non-invasive sampling method. This thesis is supervised by Antoine Frénoy, Nelle Varoquaux and Philippe Cinquin